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mmu_circLmbr1_438_1
Basic information of circular RNA
PanCircBase ID:
mmu_circLmbr1_438_1
mm39_Chr. Position ID:
chr5|29468392|29528822|-
Gene name:
Lmbr1
Transcript:
ENSMUST00000198105.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
10,9,8,7,6,5
Exon/intron offsets:
0,23996,27878,28757,29428,60407
Genomic length:
60430
Exon/intron sizes in nt:
81,73,65,69,127,23
Flanking exon/introns:
chr5:29463753-29468392|chr5:29528822-29551764
Splice length:
438
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AAGGTTTTGCAGGCCTGAAAAAGGGAATCCGAGCCCGCATTTTGGAAACTCTGGTTATGCTGCTGCTTCTTGCGTTGCTGATTCTTGGGATGGTGTGGGTGGCTTCCGCCCTGATTGACAGTGATGCTGCCAGTATGGAGTCTTTATATGATCTCTGGGAATTCTACTTGCCCTATTTGTATTCTTGCATTTCGCTGATGGGATGCTTGCTGCTTCTCTTGTGTACTCCAGTTGGCCTGTCCCGTATGTTCACAGTCATGGGTCAGTTGCTGGTGAAGCCAGCGATTCTTGAAGACCTGGATGAACAAATTTATATGATTACTCTAGAAGAAGAAGCACTCCAGAGAAGACTACATGGGCTATCTTCATCGGTGGAGTACAATGTAATGGAATTGGAGCAAGAACTTGAGAATGTAAAGATCCTTAAGACAAAATTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGCTATCTTCATCGGTGG
59.24
TCCCAAGAATCAGCAACGCA
60.25
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGCTATCTTCATCGGTGG
59.24
CGCAAGAAGCAGCAGCATAA
59.55
157
PCR template sequence:
CTCCAGAGAAGACTACATGGGCTATCTTCATCGGTGGAGTACAATGTAATGGAATTGGAGCAAGAACTTGAGAATGTAAAGATCCTTAAGACAAAATTAGAAGGTTTTGCAGGCCTGAAAAAGGGAATCCGAGCCCGCATTTTGGAAACTCTGGTTATGCTGCTGCTTCTTGCGTTGCTGATTCTTGGGATGGTGTGGGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(2), mmu-miR-103-3p(2), mmu-miR-107-3p(2), mmu-miR-15a-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-324-5p(1), mmu-miR-215-5p(1), mmu-miR-340-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGACAAAATTAGAAGGTTTTGCAGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLMBR1_438_1_ORF_1
1.0062
0.097859962
0.948722572
819
ORF sequence:
ATGCTGCTGCTTCTTGCGTTGCTGATTCTTGGGATGGTGTGGGTGGCTTCCGCCCTGATTGACAGTGATGCTGCCAGTATGGAGTCTTTATATGATCTCTGGGAATTCTACTTGCCCTATTTGTATTCTTGCATTTCGCTGATGGGATGCTTGCTGCTTCTCTTGTGTACTCCAGTTGGCCTGTCCCGTATGTTCACAGTCATGGGTCAGTTGCTGGTGAAGCCAGCGATTCTTGAAGACCTGGATGAACAAATTTATATGATTACTCTAGAAGAAGAAGCACTCCAGAGAAGACTACATGGGCTATCTTCATCGGTGGAGTACAATGTAATGGAATTGGAGCAAGAACTTGAGAATGTAAAGATCCTTAAGACAAAATTAGAAGGTTTTGCAGGCCTGAAAAAGGGAATCCGAGCCCGCATTTTGGAAACTCTGGTTATGCTGCTGCTTCTTGCGTTGCTGATTCTTGGGATGGTGTGGGTGGCTTCCGCCCTGATTGACAGTGATGCTGCCAGTATGGAGTCTTTATATGATCTCTGGGAATTCTACTTGCCCTATTTGTATTCTTGCATTTCGCTGATGGGATGCTTGCTGCTTCTCTTGTGTACTCCAGTTGGCCTGTCCCGTATGTTCACAGTCATGGGTCAGTTGCTGGTGAAGCCAGCGATTCTTGAAGACCTGGATGAACAAATTTATATGATTACTCTAGAAGAAGAAGCACTCCAGAGAAGACTACATGGGCTATCTTCATCGGTGGAGTACAATGTAATGGAATTGGAGCAAGAACTTGAGAATGTAAAGATCCTTAAGACAAAATTA
Peptide sequence:
MLLLLALLILGMVWVASALIDSDAASMESLYDLWEFYLPYLYSCISLMGCLLLLLCTPVGLSRMFTVMGQLLVKPAILEDLDEQIYMITLEEEALQRRLHGLSSSVEYNVMELEQELENVKILKTKLEGFAGLKKGIRARILETLVMLLLLALLILGMVWVASALIDSDAASMESLYDLWEFYLPYLYSCISLMGCLLLLLCTPVGLSRMFTVMGQLLVKPAILEDLDEQIYMITLEEEALQRRLHGLSSSVEYNVMELEQELENVKILKTKL
IRESfinder result
IRESfinder score
0.688712559
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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